🧬 Seurat Preprocessing Shiny App

Welcome to the DR-scRNASeq! This app provides a user-friendly interface for performing various preprocessing and analysis tasks on single-cell RNA sequencing data using the Seurat package. Below is an overview of the workflows available in the app:

🚀 Features

1. 🗂️ Generate Your Seurat Object using Upload and Convert

• 📂 Upload Your File: Start by uploading your .h5 or .gz file containing your single-cell RNA sequencing data.
• 🔄 Convert: Press the Convert button to convert your uploaded file into a Seurat object.
• 💾 Download: Once the conversion is complete, you can download the generated Seurat object for further analysis.

2. 🧪 Perform Preprocessing on Your Seurat Object using Analyze and Process

• 📂 Upload Your .rds File: Upload your existing Seurat object stored as an .rds file.
• ⚙️ Specify Parameters: Define the desired values and parameters for preprocessing, such as normalization, scaling, and filtering criteria.
• 🔄 Process: Click the Process button to execute the preprocessing steps on your data.
• 💾 Download: After processing, download the pre-processed Seurat object for dimensionality reduction or further analysis.

3. 📊 Perform Dimensionality Reduction using Plot and Explore

• 📂 Upload Pre-Processed .rds File: Upload the pre-processed Seurat object that you obtained from the previous step.
• 🔍 Select Algorithm: Choose the dimensionality reduction algorithm (e.g., PCA, t-SNE, UMAP) you wish to apply.
• ▶️ Run: Press the Run button to perform the dimensionality reduction and generate visualizations.
• 🔎 Explore: Two tabs will appear, allowing you to explore the data through the generated plots.
• 💾 Download Plots: You will also have the option to download the plots for further analysis or presentation.